Starting phenix.real_space_refine on Tue Mar 3 23:06:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y36_33590/03_2026/7y36_33590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y36_33590/03_2026/7y36_33590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2026/7y36_33590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2026/7y36_33590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2026/7y36_33590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2026/7y36_33590.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5851 2.51 5 N 1616 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9206 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3053 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1858 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' OH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 9206 At special positions: 0 Unit cell: (124.722, 97.344, 152.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1681 8.00 N 1616 7.00 C 5851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 294.2 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 43.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 33 through 57 removed outlier: 3.522A pdb=" N ARG R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 172 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.348A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.681A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.067A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.566A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 420 through 424 removed outlier: 3.633A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.605A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.925A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.864A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.556A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.615A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.002A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.797A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.787A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.093A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.690A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.641A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.812A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.502A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.786A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.591A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.545A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.522A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.170A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1503 1.31 - 1.44: 2663 1.44 - 1.56: 5159 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 9407 Sorted by residual: bond pdb=" C GLN A 227 " pdb=" N ARG A 228 " ideal model delta sigma weight residual 1.330 1.403 -0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.98e+01 bond pdb=" CA THR R 178 " pdb=" C THR R 178 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.34e-02 5.57e+03 1.59e+01 bond pdb=" N LEU R 174 " pdb=" CA LEU R 174 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.23e-02 6.61e+03 1.58e+01 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.22e-02 6.72e+03 1.42e+01 ... (remaining 9402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12457 2.04 - 4.08: 233 4.08 - 6.12: 28 6.12 - 8.17: 10 8.17 - 10.21: 4 Bond angle restraints: 12732 Sorted by residual: angle pdb=" N GLU R 169 " pdb=" CA GLU R 169 " pdb=" C GLU R 169 " ideal model delta sigma weight residual 111.71 102.90 8.81 1.15e+00 7.56e-01 5.87e+01 angle pdb=" C GLN A 227 " pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 121.06 131.27 -10.21 1.88e+00 2.83e-01 2.95e+01 angle pdb=" C LEU P 24 " pdb=" N ARG P 25 " pdb=" CA ARG P 25 " ideal model delta sigma weight residual 120.44 113.12 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" N LEU R 174 " pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 111.33 117.63 -6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" N LYS R 172 " pdb=" CA LYS R 172 " pdb=" C LYS R 172 " ideal model delta sigma weight residual 112.38 118.55 -6.17 1.22e+00 6.72e-01 2.56e+01 ... (remaining 12727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5106 17.75 - 35.51: 391 35.51 - 53.26: 69 53.26 - 71.01: 8 71.01 - 88.77: 5 Dihedral angle restraints: 5579 sinusoidal: 2231 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CA CYS R 351 " pdb=" C CYS R 351 " pdb=" N TRP R 352 " pdb=" CA TRP R 352 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1097 0.056 - 0.111: 260 0.111 - 0.167: 40 0.167 - 0.223: 6 0.223 - 0.278: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA LEU R 174 " pdb=" N LEU R 174 " pdb=" C LEU R 174 " pdb=" CB LEU R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR R 178 " pdb=" N THR R 178 " pdb=" C THR R 178 " pdb=" CB THR R 178 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1402 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 168 " 0.035 2.00e-02 2.50e+03 7.17e-02 5.15e+01 pdb=" C SER R 168 " -0.124 2.00e-02 2.50e+03 pdb=" O SER R 168 " 0.048 2.00e-02 2.50e+03 pdb=" N GLU R 169 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO B 236 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.016 2.00e-02 2.50e+03 1.54e-02 4.73e+00 pdb=" CG TYR B 59 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 8791 3.25 - 3.80: 14683 3.80 - 4.35: 19212 4.35 - 4.90: 32425 Nonbonded interactions: 75371 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" O ASP R 113 " pdb=" CG1 VAL P 31 " model vdw 2.178 3.460 nonbonded pdb=" OG1 THR R 218 " pdb=" OE2 GLU R 317 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.207 3.040 nonbonded pdb=" CG2 ILE R 115 " pdb=" NZ LYS P 27 " model vdw 2.229 3.540 ... (remaining 75366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.171 9414 Z= 0.377 Angle : 0.746 13.025 12744 Z= 0.450 Chirality : 0.049 0.278 1405 Planarity : 0.005 0.072 1621 Dihedral : 12.892 88.766 3395 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.22), residues: 1127 helix: -0.23 (0.22), residues: 449 sheet: -0.68 (0.31), residues: 227 loop : -1.41 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 72 TYR 0.038 0.002 TYR B 59 PHE 0.021 0.002 PHE R 335 TRP 0.024 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 9407) covalent geometry : angle 0.73202 (12732) SS BOND : bond 0.00985 ( 6) SS BOND : angle 4.71062 ( 12) hydrogen bonds : bond 0.16462 ( 472) hydrogen bonds : angle 6.24254 ( 1359) Misc. bond : bond 0.17053 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 0.5254 time to fit residues: 173.9411 Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 458 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 41 HIS B 62 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 176 GLN B 266 HIS B 313 ASN N 77 ASN N 82 GLN N 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.183647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153266 restraints weight = 15786.491| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.88 r_work: 0.3852 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 9414 Z= 0.220 Angle : 0.744 12.332 12744 Z= 0.392 Chirality : 0.046 0.165 1405 Planarity : 0.005 0.083 1621 Dihedral : 4.896 26.745 1261 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.75 % Allowed : 16.16 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.24), residues: 1127 helix: 0.93 (0.24), residues: 451 sheet: -0.15 (0.32), residues: 218 loop : -0.98 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 20 TYR 0.040 0.002 TYR R 191 PHE 0.036 0.002 PHE R 335 TRP 0.019 0.002 TRP B 82 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9407) covalent geometry : angle 0.74213 (12732) SS BOND : bond 0.01622 ( 6) SS BOND : angle 2.06032 ( 12) hydrogen bonds : bond 0.04949 ( 472) hydrogen bonds : angle 4.75226 ( 1359) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7916 (ttp) cc_final: 0.7573 (tpp) REVERT: R 214 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7811 (mtp85) REVERT: R 281 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5286 (t) REVERT: R 322 TRP cc_start: 0.5922 (t60) cc_final: 0.5404 (t60) REVERT: R 441 MET cc_start: 0.7667 (mmm) cc_final: 0.7270 (mmm) REVERT: R 469 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8075 (mm-30) REVERT: P 8 MET cc_start: 0.6412 (ttp) cc_final: 0.5722 (tmm) REVERT: P 11 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5925 (tp) REVERT: A 265 ARG cc_start: 0.6085 (pmt170) cc_final: 0.5863 (ptt-90) REVERT: A 343 ASP cc_start: 0.8537 (m-30) cc_final: 0.8002 (m-30) REVERT: A 347 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7485 (ptp-110) REVERT: A 363 PHE cc_start: 0.8549 (m-80) cc_final: 0.8261 (m-80) REVERT: A 381 ASP cc_start: 0.8587 (t70) cc_final: 0.8285 (t0) REVERT: B 19 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7226 (ptp-110) REVERT: B 81 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5877 (pt) REVERT: B 123 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7407 (pp) REVERT: B 187 VAL cc_start: 0.6277 (OUTLIER) cc_final: 0.5719 (p) REVERT: B 188 MET cc_start: 0.8190 (mmm) cc_final: 0.7981 (mmm) REVERT: B 290 ASP cc_start: 0.7203 (m-30) cc_final: 0.6816 (m-30) REVERT: N 60 TYR cc_start: 0.8298 (m-80) cc_final: 0.7995 (m-80) REVERT: N 76 LYS cc_start: 0.8384 (tptp) cc_final: 0.8159 (tppp) REVERT: N 87 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7792 (ptpp) REVERT: N 120 GLN cc_start: 0.7396 (mm110) cc_final: 0.7083 (mm-40) outliers start: 47 outliers final: 12 residues processed: 289 average time/residue: 0.4668 time to fit residues: 145.2722 Evaluate side-chains 219 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.1980 chunk 108 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 266 HIS B 295 ASN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125156 restraints weight = 14997.125| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.71 r_work: 0.3469 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9414 Z= 0.185 Angle : 0.703 10.520 12744 Z= 0.369 Chirality : 0.045 0.165 1405 Planarity : 0.005 0.062 1621 Dihedral : 4.797 37.374 1259 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.45 % Allowed : 19.90 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1127 helix: 1.30 (0.24), residues: 456 sheet: -0.09 (0.33), residues: 223 loop : -0.79 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.030 0.002 TYR R 191 PHE 0.016 0.002 PHE R 335 TRP 0.022 0.002 TRP N 36 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9407) covalent geometry : angle 0.70094 (12732) SS BOND : bond 0.01796 ( 6) SS BOND : angle 1.71127 ( 12) hydrogen bonds : bond 0.04798 ( 472) hydrogen bonds : angle 4.57667 ( 1359) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8407 (ttp) cc_final: 0.7773 (pmm) REVERT: R 214 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7887 (mtp85) REVERT: R 278 TYR cc_start: 0.5881 (p90) cc_final: 0.5430 (m-80) REVERT: R 322 TRP cc_start: 0.6009 (t60) cc_final: 0.5439 (t60) REVERT: R 358 ASN cc_start: 0.7823 (m-40) cc_final: 0.7529 (t0) REVERT: R 441 MET cc_start: 0.8544 (mmm) cc_final: 0.8289 (mmm) REVERT: R 469 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8262 (mm-30) REVERT: P 8 MET cc_start: 0.8077 (ttp) cc_final: 0.7768 (tmm) REVERT: A 248 VAL cc_start: 0.8901 (t) cc_final: 0.8574 (m) REVERT: A 265 ARG cc_start: 0.6768 (pmt170) cc_final: 0.6485 (ptt-90) REVERT: A 299 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8803 (pt0) REVERT: A 309 GLU cc_start: 0.8194 (pm20) cc_final: 0.7928 (mt-10) REVERT: A 368 ASP cc_start: 0.4760 (m-30) cc_final: 0.4473 (t0) REVERT: A 370 GLU cc_start: 0.7206 (mp0) cc_final: 0.6844 (mp0) REVERT: A 381 ASP cc_start: 0.8283 (t70) cc_final: 0.7914 (t0) REVERT: A 389 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8311 (ttm110) REVERT: B 19 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7345 (ptp-110) REVERT: B 45 MET cc_start: 0.9365 (mtt) cc_final: 0.9148 (mtt) REVERT: B 89 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7494 (ptpp) REVERT: B 138 GLU cc_start: 0.8599 (mp0) cc_final: 0.8374 (mp0) REVERT: B 176 GLN cc_start: 0.7833 (tt0) cc_final: 0.7081 (tm130) REVERT: B 201 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.7378 (p) REVERT: B 230 ASN cc_start: 0.8676 (t0) cc_final: 0.8346 (m-40) REVERT: B 292 PHE cc_start: 0.8874 (m-10) cc_final: 0.8288 (m-80) REVERT: B 312 ASP cc_start: 0.8076 (t0) cc_final: 0.7588 (t0) REVERT: G 57 SER cc_start: 0.8976 (t) cc_final: 0.8430 (p) REVERT: G 62 ARG cc_start: 0.7191 (tpt-90) cc_final: 0.6807 (tpp80) REVERT: N 60 TYR cc_start: 0.8715 (m-80) cc_final: 0.8093 (m-80) REVERT: N 83 MET cc_start: 0.6224 (mtp) cc_final: 0.5990 (mtt) REVERT: N 87 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7784 (ptpp) REVERT: N 89 GLU cc_start: 0.9098 (tp30) cc_final: 0.8762 (tp30) outliers start: 54 outliers final: 21 residues processed: 282 average time/residue: 0.5473 time to fit residues: 164.3920 Evaluate side-chains 222 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 9 HIS P 10 ASN A 236 GLN B 6 GLN B 293 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123732 restraints weight = 15108.253| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.70 r_work: 0.3468 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.9153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9414 Z= 0.128 Angle : 0.622 10.165 12744 Z= 0.324 Chirality : 0.043 0.157 1405 Planarity : 0.004 0.034 1621 Dihedral : 4.360 29.003 1259 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.85 % Allowed : 24.65 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1127 helix: 1.77 (0.25), residues: 453 sheet: 0.26 (0.33), residues: 226 loop : -0.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.025 0.001 TYR R 191 PHE 0.013 0.001 PHE R 335 TRP 0.016 0.001 TRP P 23 HIS 0.003 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9407) covalent geometry : angle 0.62022 (12732) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.51031 ( 12) hydrogen bonds : bond 0.04027 ( 472) hydrogen bonds : angle 4.23680 ( 1359) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 214 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7859 (mtp85) REVERT: R 322 TRP cc_start: 0.6217 (t60) cc_final: 0.5589 (t60) REVERT: R 349 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8078 (p) REVERT: R 358 ASN cc_start: 0.7804 (m-40) cc_final: 0.7571 (t0) REVERT: R 469 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8495 (mm-30) REVERT: P 8 MET cc_start: 0.8192 (ttp) cc_final: 0.7822 (ttm) REVERT: A 35 GLN cc_start: 0.8269 (mt0) cc_final: 0.7792 (mp10) REVERT: A 265 ARG cc_start: 0.6793 (pmt170) cc_final: 0.6484 (ptt-90) REVERT: A 309 GLU cc_start: 0.8194 (pm20) cc_final: 0.7951 (mt-10) REVERT: A 368 ASP cc_start: 0.4728 (m-30) cc_final: 0.4336 (t0) REVERT: A 370 GLU cc_start: 0.7256 (mp0) cc_final: 0.6781 (mp0) REVERT: A 378 ASP cc_start: 0.8159 (m-30) cc_final: 0.7928 (m-30) REVERT: A 381 ASP cc_start: 0.8343 (t70) cc_final: 0.7985 (t0) REVERT: A 389 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8292 (ttm110) REVERT: B 19 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7175 (ptp-110) REVERT: B 57 LYS cc_start: 0.8570 (pttm) cc_final: 0.8219 (ptpp) REVERT: B 76 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8336 (p0) REVERT: B 123 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7924 (mm) REVERT: B 176 GLN cc_start: 0.8021 (tt0) cc_final: 0.7265 (tm130) REVERT: B 217 MET cc_start: 0.8641 (mmm) cc_final: 0.8340 (mmm) REVERT: B 229 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7787 (mt) REVERT: B 230 ASN cc_start: 0.8690 (t0) cc_final: 0.8314 (m-40) REVERT: B 292 PHE cc_start: 0.8859 (m-10) cc_final: 0.8335 (m-80) REVERT: B 312 ASP cc_start: 0.8128 (t0) cc_final: 0.7595 (t0) REVERT: G 62 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.6720 (tpp80) REVERT: N 38 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7849 (ptt180) REVERT: N 60 TYR cc_start: 0.8704 (m-80) cc_final: 0.8084 (m-80) REVERT: N 73 ASP cc_start: 0.5644 (p0) cc_final: 0.5357 (p0) REVERT: N 76 LYS cc_start: 0.8892 (tppp) cc_final: 0.8476 (ttmt) REVERT: N 87 LYS cc_start: 0.8220 (ptpp) cc_final: 0.7873 (ptpp) REVERT: N 89 GLU cc_start: 0.9092 (tp30) cc_final: 0.8726 (tp30) REVERT: N 109 ASP cc_start: 0.7346 (p0) cc_final: 0.6586 (p0) outliers start: 48 outliers final: 21 residues processed: 240 average time/residue: 0.5576 time to fit residues: 142.3163 Evaluate side-chains 212 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS P 33 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105715 restraints weight = 14917.495| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.44 r_work: 0.3213 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 1.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9414 Z= 0.226 Angle : 0.746 10.124 12744 Z= 0.392 Chirality : 0.048 0.239 1405 Planarity : 0.005 0.046 1621 Dihedral : 4.879 30.505 1259 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.97 % Allowed : 23.54 % Favored : 69.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1127 helix: 1.46 (0.24), residues: 453 sheet: 0.11 (0.33), residues: 228 loop : -0.57 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.027 0.002 TYR R 191 PHE 0.020 0.002 PHE G 61 TRP 0.027 0.002 TRP N 36 HIS 0.009 0.002 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9407) covalent geometry : angle 0.74446 (12732) SS BOND : bond 0.00490 ( 6) SS BOND : angle 1.63529 ( 12) hydrogen bonds : bond 0.05576 ( 472) hydrogen bonds : angle 4.62954 ( 1359) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 THR cc_start: 0.8613 (m) cc_final: 0.8373 (p) REVERT: R 214 ARG cc_start: 0.8439 (mtp85) cc_final: 0.7833 (mtp85) REVERT: R 469 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8582 (mm-30) REVERT: P 8 MET cc_start: 0.8716 (ttp) cc_final: 0.8386 (ttm) REVERT: A 31 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8842 (mm-40) REVERT: A 35 GLN cc_start: 0.8523 (mt0) cc_final: 0.7963 (mp10) REVERT: A 213 GLN cc_start: 0.9101 (tt0) cc_final: 0.8826 (tm-30) REVERT: A 265 ARG cc_start: 0.7062 (pmt170) cc_final: 0.6700 (ptt-90) REVERT: A 297 LEU cc_start: 0.7513 (mt) cc_final: 0.7033 (mt) REVERT: A 299 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8869 (pm20) REVERT: A 309 GLU cc_start: 0.8344 (pm20) cc_final: 0.7966 (mt-10) REVERT: A 344 GLU cc_start: 0.8613 (tp30) cc_final: 0.8337 (tp30) REVERT: A 381 ASP cc_start: 0.8344 (t70) cc_final: 0.8016 (t0) REVERT: B 22 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6228 (mpt-90) REVERT: B 37 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 59 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 76 ASP cc_start: 0.8712 (p0) cc_final: 0.8345 (p0) REVERT: B 156 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: B 189 SER cc_start: 0.8979 (t) cc_final: 0.8642 (t) REVERT: B 197 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8180 (mmm-85) REVERT: B 217 MET cc_start: 0.8570 (mmm) cc_final: 0.8281 (mpp) REVERT: B 219 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8388 (mmt90) REVERT: B 230 ASN cc_start: 0.8881 (t0) cc_final: 0.8601 (m-40) REVERT: B 304 ARG cc_start: 0.8690 (mtp180) cc_final: 0.8081 (ttm110) REVERT: B 312 ASP cc_start: 0.8483 (t0) cc_final: 0.8023 (t0) REVERT: G 27 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7902 (mpt90) REVERT: G 58 GLU cc_start: 0.8012 (mp0) cc_final: 0.7689 (mm-30) REVERT: G 62 ARG cc_start: 0.7200 (tpt-90) cc_final: 0.6833 (tpp80) REVERT: N 38 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8321 (ptm160) REVERT: N 89 GLU cc_start: 0.9104 (tp30) cc_final: 0.8754 (tp30) REVERT: N 93 VAL cc_start: 0.8369 (t) cc_final: 0.8106 (p) REVERT: N 109 ASP cc_start: 0.7787 (p0) cc_final: 0.7290 (p0) REVERT: N 110 VAL cc_start: 0.8955 (t) cc_final: 0.8671 (m) REVERT: N 117 TYR cc_start: 0.8056 (m-80) cc_final: 0.7819 (m-80) outliers start: 69 outliers final: 27 residues processed: 292 average time/residue: 0.5568 time to fit residues: 173.0615 Evaluate side-chains 229 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 0.0040 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 348 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109368 restraints weight = 14783.779| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.46 r_work: 0.3279 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 1.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9414 Z= 0.133 Angle : 0.654 11.080 12744 Z= 0.339 Chirality : 0.043 0.186 1405 Planarity : 0.004 0.042 1621 Dihedral : 4.452 26.951 1259 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.35 % Allowed : 27.47 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1127 helix: 1.94 (0.24), residues: 450 sheet: 0.65 (0.35), residues: 215 loop : -0.69 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 20 TYR 0.023 0.001 TYR R 191 PHE 0.021 0.001 PHE R 335 TRP 0.024 0.001 TRP P 23 HIS 0.004 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9407) covalent geometry : angle 0.65269 (12732) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.48435 ( 12) hydrogen bonds : bond 0.04193 ( 472) hydrogen bonds : angle 4.27483 ( 1359) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.7392 (tpp-160) REVERT: R 203 THR cc_start: 0.8623 (m) cc_final: 0.8392 (p) REVERT: R 214 ARG cc_start: 0.8354 (mtp85) cc_final: 0.7899 (mtp85) REVERT: R 349 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9027 (p) REVERT: R 352 TRP cc_start: 0.8620 (m-10) cc_final: 0.8296 (m-10) REVERT: R 358 ASN cc_start: 0.8211 (m-40) cc_final: 0.7617 (t0) REVERT: R 469 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8495 (mm-30) REVERT: A 31 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8733 (mm110) REVERT: A 35 GLN cc_start: 0.8552 (mt0) cc_final: 0.7994 (mp10) REVERT: A 213 GLN cc_start: 0.9112 (tt0) cc_final: 0.8842 (tm-30) REVERT: A 265 ARG cc_start: 0.7145 (pmt170) cc_final: 0.6829 (ptt90) REVERT: A 309 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: A 344 GLU cc_start: 0.8662 (tp30) cc_final: 0.8383 (tp30) REVERT: A 381 ASP cc_start: 0.8380 (t70) cc_final: 0.8049 (t0) REVERT: B 59 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: B 76 ASP cc_start: 0.8665 (p0) cc_final: 0.8177 (p0) REVERT: B 135 VAL cc_start: 0.8848 (t) cc_final: 0.8600 (t) REVERT: B 197 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: B 219 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8521 (mmt90) REVERT: B 230 ASN cc_start: 0.8800 (t0) cc_final: 0.8559 (m110) REVERT: B 233 CYS cc_start: 0.9268 (t) cc_final: 0.8871 (t) REVERT: B 234 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: B 304 ARG cc_start: 0.8573 (mtp180) cc_final: 0.8093 (ttm110) REVERT: B 312 ASP cc_start: 0.8488 (t0) cc_final: 0.8202 (t0) REVERT: G 58 GLU cc_start: 0.8013 (mp0) cc_final: 0.7646 (mm-30) REVERT: G 62 ARG cc_start: 0.7085 (tpt-90) cc_final: 0.6769 (tpp80) REVERT: N 38 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8350 (ptm160) REVERT: N 73 ASP cc_start: 0.5588 (p0) cc_final: 0.5300 (p0) REVERT: N 76 LYS cc_start: 0.9178 (tppp) cc_final: 0.8452 (ttmp) REVERT: N 89 GLU cc_start: 0.9102 (tp30) cc_final: 0.8750 (tp30) REVERT: N 109 ASP cc_start: 0.7758 (p0) cc_final: 0.7097 (p0) REVERT: N 123 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7752 (tm-30) outliers start: 53 outliers final: 24 residues processed: 253 average time/residue: 0.5742 time to fit residues: 154.0708 Evaluate side-chains 227 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 266 HIS N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108546 restraints weight = 14912.383| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.44 r_work: 0.3269 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 1.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9414 Z= 0.142 Angle : 0.660 10.017 12744 Z= 0.343 Chirality : 0.043 0.185 1405 Planarity : 0.004 0.036 1621 Dihedral : 4.371 26.077 1259 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.65 % Allowed : 29.19 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1127 helix: 1.98 (0.25), residues: 450 sheet: 0.60 (0.35), residues: 221 loop : -0.58 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 13 TYR 0.024 0.001 TYR R 191 PHE 0.025 0.001 PHE R 335 TRP 0.025 0.001 TRP P 23 HIS 0.010 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9407) covalent geometry : angle 0.65854 (12732) SS BOND : bond 0.00270 ( 6) SS BOND : angle 1.55730 ( 12) hydrogen bonds : bond 0.04128 ( 472) hydrogen bonds : angle 4.23838 ( 1359) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7810 (tpp) cc_final: 0.7489 (tpp) REVERT: R 203 THR cc_start: 0.8628 (m) cc_final: 0.8370 (p) REVERT: R 214 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7888 (mtp85) REVERT: R 358 ASN cc_start: 0.8238 (m-40) cc_final: 0.7660 (t0) REVERT: R 431 GLU cc_start: 0.8124 (pp20) cc_final: 0.7482 (tm-30) REVERT: R 469 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8551 (mm-30) REVERT: A 31 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8755 (mm-40) REVERT: A 35 GLN cc_start: 0.8562 (mt0) cc_final: 0.7980 (mp10) REVERT: A 210 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8118 (p) REVERT: A 213 GLN cc_start: 0.9061 (tt0) cc_final: 0.8757 (tm-30) REVERT: A 265 ARG cc_start: 0.7129 (pmt170) cc_final: 0.6850 (ptt180) REVERT: A 309 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: A 344 GLU cc_start: 0.8701 (tp30) cc_final: 0.8374 (tp30) REVERT: A 381 ASP cc_start: 0.8356 (t70) cc_final: 0.8015 (t0) REVERT: B 59 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: B 76 ASP cc_start: 0.8565 (p0) cc_final: 0.8133 (p0) REVERT: B 197 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8157 (mmm-85) REVERT: B 219 ARG cc_start: 0.8839 (mmm-85) cc_final: 0.8466 (mmt90) REVERT: B 233 CYS cc_start: 0.9263 (t) cc_final: 0.8830 (t) REVERT: B 234 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: B 304 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8390 (ttm110) REVERT: B 312 ASP cc_start: 0.8488 (t0) cc_final: 0.8166 (t0) REVERT: G 58 GLU cc_start: 0.8076 (mp0) cc_final: 0.7700 (mm-30) REVERT: N 38 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8383 (ptm160) REVERT: N 76 LYS cc_start: 0.9203 (tppp) cc_final: 0.8750 (ttmp) REVERT: N 89 GLU cc_start: 0.9113 (tp30) cc_final: 0.8723 (pp20) REVERT: N 123 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7980 (tm-30) outliers start: 46 outliers final: 18 residues processed: 233 average time/residue: 0.5513 time to fit residues: 136.8017 Evaluate side-chains 223 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 91 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 0.0020 chunk 55 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 176 GLN B 230 ASN B 266 HIS N 77 ASN N 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.144851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110165 restraints weight = 14735.740| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.48 r_work: 0.3294 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 1.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9414 Z= 0.130 Angle : 0.659 10.999 12744 Z= 0.339 Chirality : 0.043 0.356 1405 Planarity : 0.004 0.037 1621 Dihedral : 4.263 24.440 1259 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.54 % Allowed : 30.00 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1127 helix: 2.15 (0.25), residues: 443 sheet: 0.89 (0.35), residues: 213 loop : -0.57 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 13 TYR 0.025 0.001 TYR R 191 PHE 0.027 0.001 PHE R 335 TRP 0.025 0.001 TRP P 23 HIS 0.008 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9407) covalent geometry : angle 0.65814 (12732) SS BOND : bond 0.00257 ( 6) SS BOND : angle 1.47767 ( 12) hydrogen bonds : bond 0.03874 ( 472) hydrogen bonds : angle 4.17773 ( 1359) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7807 (tpp) cc_final: 0.7532 (tpp) REVERT: R 203 THR cc_start: 0.8642 (m) cc_final: 0.8382 (p) REVERT: R 358 ASN cc_start: 0.8147 (m-40) cc_final: 0.7602 (t0) REVERT: R 431 GLU cc_start: 0.8071 (pp20) cc_final: 0.7355 (tm-30) REVERT: A 31 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8758 (mm-40) REVERT: A 35 GLN cc_start: 0.8619 (mt0) cc_final: 0.8048 (mp10) REVERT: A 213 GLN cc_start: 0.9083 (tt0) cc_final: 0.8854 (tm-30) REVERT: A 265 ARG cc_start: 0.7179 (pmt170) cc_final: 0.6950 (ptt90) REVERT: A 299 GLU cc_start: 0.8428 (pp20) cc_final: 0.7925 (pm20) REVERT: A 309 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: A 344 GLU cc_start: 0.8645 (tp30) cc_final: 0.8354 (tp30) REVERT: A 381 ASP cc_start: 0.8411 (t70) cc_final: 0.8072 (t0) REVERT: B 59 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: B 76 ASP cc_start: 0.8561 (p0) cc_final: 0.8269 (p0) REVERT: B 197 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8079 (mmm-85) REVERT: B 211 TRP cc_start: 0.8101 (m-90) cc_final: 0.7859 (m100) REVERT: B 219 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8258 (mmt90) REVERT: B 233 CYS cc_start: 0.9272 (t) cc_final: 0.8835 (t) REVERT: B 234 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: B 304 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8333 (ttm110) REVERT: G 58 GLU cc_start: 0.8091 (mp0) cc_final: 0.7692 (mm-30) REVERT: N 38 ARG cc_start: 0.8719 (ptt-90) cc_final: 0.8389 (ptm160) REVERT: N 73 ASP cc_start: 0.5636 (p0) cc_final: 0.4968 (p0) REVERT: N 76 LYS cc_start: 0.9337 (tppp) cc_final: 0.8436 (ttpp) REVERT: N 89 GLU cc_start: 0.9118 (tp30) cc_final: 0.8801 (pp20) outliers start: 35 outliers final: 21 residues processed: 232 average time/residue: 0.5517 time to fit residues: 136.3780 Evaluate side-chains 223 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 176 GLN B 230 ASN B 266 HIS N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105693 restraints weight = 15018.868| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.46 r_work: 0.3229 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 1.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9414 Z= 0.154 Angle : 0.687 10.500 12744 Z= 0.354 Chirality : 0.045 0.395 1405 Planarity : 0.004 0.036 1621 Dihedral : 4.271 23.350 1259 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.03 % Allowed : 31.21 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1127 helix: 2.02 (0.24), residues: 448 sheet: 0.85 (0.35), residues: 214 loop : -0.55 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 343 TYR 0.025 0.001 TYR R 191 PHE 0.028 0.001 PHE R 335 TRP 0.029 0.001 TRP P 23 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9407) covalent geometry : angle 0.68572 (12732) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.47121 ( 12) hydrogen bonds : bond 0.04217 ( 472) hydrogen bonds : angle 4.14479 ( 1359) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7941 (tpp) cc_final: 0.7691 (tpp) REVERT: R 203 THR cc_start: 0.8623 (m) cc_final: 0.8344 (p) REVERT: R 358 ASN cc_start: 0.8199 (m-40) cc_final: 0.7693 (t0) REVERT: A 31 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8763 (mm-40) REVERT: A 35 GLN cc_start: 0.8648 (mt0) cc_final: 0.8070 (mp10) REVERT: A 213 GLN cc_start: 0.9056 (tt0) cc_final: 0.8786 (tm-30) REVERT: A 265 ARG cc_start: 0.6969 (pmt170) cc_final: 0.6698 (ptt90) REVERT: A 299 GLU cc_start: 0.8423 (pp20) cc_final: 0.8077 (pp20) REVERT: A 309 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: A 344 GLU cc_start: 0.8714 (tp30) cc_final: 0.8402 (tp30) REVERT: A 381 ASP cc_start: 0.8359 (t70) cc_final: 0.8062 (t0) REVERT: A 389 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7954 (ttm110) REVERT: B 59 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: B 76 ASP cc_start: 0.8675 (p0) cc_final: 0.8296 (p0) REVERT: B 197 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8121 (mmm-85) REVERT: B 211 TRP cc_start: 0.8083 (m-90) cc_final: 0.7554 (m100) REVERT: B 212 ASP cc_start: 0.8194 (t0) cc_final: 0.7582 (t0) REVERT: B 217 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7319 (pmt) REVERT: B 255 LEU cc_start: 0.8756 (mp) cc_final: 0.8547 (mt) REVERT: B 304 ARG cc_start: 0.8681 (mtp180) cc_final: 0.8287 (ttm110) REVERT: B 314 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7908 (tmm-80) REVERT: G 13 ARG cc_start: 0.7302 (tmm-80) cc_final: 0.7092 (ptp-170) REVERT: G 58 GLU cc_start: 0.8201 (mp0) cc_final: 0.7786 (mm-30) REVERT: N 7 SER cc_start: 0.8251 (m) cc_final: 0.7948 (p) REVERT: N 38 ARG cc_start: 0.8747 (ptt-90) cc_final: 0.8489 (ptm160) REVERT: N 73 ASP cc_start: 0.5658 (p0) cc_final: 0.4963 (p0) REVERT: N 76 LYS cc_start: 0.9344 (tppp) cc_final: 0.8474 (ttpp) REVERT: N 106 ASP cc_start: 0.8860 (p0) cc_final: 0.8558 (p0) REVERT: N 117 TYR cc_start: 0.8132 (m-80) cc_final: 0.7895 (m-80) outliers start: 30 outliers final: 14 residues processed: 225 average time/residue: 0.5915 time to fit residues: 141.3673 Evaluate side-chains 212 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 420 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 32 GLN B 266 HIS N 77 ASN N 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105344 restraints weight = 15060.620| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.46 r_work: 0.3210 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 1.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9414 Z= 0.156 Angle : 0.724 19.357 12744 Z= 0.368 Chirality : 0.044 0.189 1405 Planarity : 0.004 0.088 1621 Dihedral : 4.295 19.438 1259 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.73 % Allowed : 31.72 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1127 helix: 2.06 (0.24), residues: 444 sheet: 0.74 (0.35), residues: 218 loop : -0.51 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 8 TYR 0.024 0.001 TYR R 191 PHE 0.028 0.001 PHE R 335 TRP 0.025 0.001 TRP P 23 HIS 0.006 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9407) covalent geometry : angle 0.72270 (12732) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.61165 ( 12) hydrogen bonds : bond 0.04231 ( 472) hydrogen bonds : angle 4.16198 ( 1359) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 138 PHE cc_start: 0.7438 (m-80) cc_final: 0.7099 (m-80) REVERT: R 203 THR cc_start: 0.8603 (m) cc_final: 0.8326 (p) REVERT: R 358 ASN cc_start: 0.8092 (m-40) cc_final: 0.7642 (t0) REVERT: R 431 GLU cc_start: 0.8347 (pt0) cc_final: 0.7957 (pp20) REVERT: P 8 MET cc_start: 0.8298 (ttm) cc_final: 0.8096 (ttm) REVERT: A 31 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8768 (mm-40) REVERT: A 35 GLN cc_start: 0.8623 (mt0) cc_final: 0.8043 (mp10) REVERT: A 213 GLN cc_start: 0.9105 (tt0) cc_final: 0.8847 (tm-30) REVERT: A 265 ARG cc_start: 0.6945 (pmt170) cc_final: 0.6636 (ptt90) REVERT: A 299 GLU cc_start: 0.8466 (pp20) cc_final: 0.8177 (pp20) REVERT: A 309 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: A 344 GLU cc_start: 0.8706 (tp30) cc_final: 0.8286 (tp30) REVERT: A 381 ASP cc_start: 0.8380 (t70) cc_final: 0.8087 (t0) REVERT: A 389 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7922 (ttm110) REVERT: B 59 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 76 ASP cc_start: 0.8588 (p0) cc_final: 0.8235 (p0) REVERT: B 197 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: B 211 TRP cc_start: 0.8088 (m-90) cc_final: 0.7673 (m100) REVERT: B 215 GLU cc_start: 0.8471 (mp0) cc_final: 0.7858 (pm20) REVERT: B 217 MET cc_start: 0.7433 (pmt) cc_final: 0.6291 (pmt) REVERT: B 255 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (mt) REVERT: B 304 ARG cc_start: 0.8687 (mtp180) cc_final: 0.8357 (ttm110) REVERT: B 314 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (tmm-80) REVERT: G 36 ASP cc_start: 0.8488 (t0) cc_final: 0.8244 (m-30) REVERT: G 58 GLU cc_start: 0.8197 (mp0) cc_final: 0.7779 (mm-30) REVERT: N 7 SER cc_start: 0.8027 (m) cc_final: 0.7646 (p) REVERT: N 38 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.8414 (ptm160) REVERT: N 73 ASP cc_start: 0.5492 (p0) cc_final: 0.5277 (p0) REVERT: N 76 LYS cc_start: 0.9329 (tppp) cc_final: 0.8565 (ttmt) REVERT: N 106 ASP cc_start: 0.8713 (p0) cc_final: 0.8437 (p0) REVERT: N 117 TYR cc_start: 0.8062 (m-80) cc_final: 0.7763 (m-80) REVERT: N 123 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8056 (tm-30) outliers start: 27 outliers final: 16 residues processed: 217 average time/residue: 0.5586 time to fit residues: 128.8097 Evaluate side-chains 220 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 266 HIS N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.142096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108256 restraints weight = 14828.196| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.47 r_work: 0.3303 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 1.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9414 Z= 0.135 Angle : 0.710 20.160 12744 Z= 0.362 Chirality : 0.044 0.186 1405 Planarity : 0.004 0.038 1621 Dihedral : 4.178 18.557 1259 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.73 % Allowed : 31.92 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1127 helix: 2.00 (0.24), residues: 447 sheet: 0.73 (0.35), residues: 220 loop : -0.47 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 8 TYR 0.025 0.001 TYR R 191 PHE 0.030 0.001 PHE R 335 TRP 0.030 0.001 TRP P 23 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9407) covalent geometry : angle 0.70869 (12732) SS BOND : bond 0.00231 ( 6) SS BOND : angle 1.45247 ( 12) hydrogen bonds : bond 0.03907 ( 472) hydrogen bonds : angle 4.14717 ( 1359) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4005.60 seconds wall clock time: 68 minutes 46.16 seconds (4126.16 seconds total)